This vignette will show you how to convert networks between graphNEL
and Cytoscape.
Installation
if(!"RCy3" %in% installed.packages()){
install.packages("BiocManager")
BiocManager::install("RCy3")
}
library(RCy3)
Required Software
The whole point of RCy3 is to connect with Cytoscape. You will need
to install and launch Cytoscape:
From graphNEL to Cytoscape
The graph package is a popular network tool among R users. With RCy3,
you can easily translate graphNEL networks to Cytoscape networks!
Create a simple GraphNEL object
Now pass it along to Cytoscape:
createNetworkFromGraph(g,"myGraph")
From Cytoscape to GraphNEL
Inversely, you can use createGraphFromNetwork() in RCy3 to retreive
vertex (node) and edge data.frames to construct a GraphNEL object.
g2 <- createGraphFromNetwork("myGraph")
Compare the round-trip result for yourself…
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